Presentation

Introduction: Paper and background

  • Circulating Exosomal microRNAs as Predictive Biomarkers of Neoadjuvant Chemotherapy Response in Breast Cancer

Neoadjuvant chemotherapy (NACT) | an increasingly used approach for treatment of breast cancer |
Circulating Exosomal microRNAs(miRNA) | small RNA molecules circulating in bodily fluids, potentially serving as biomarkers for treatment response after NACT |
Pathological Complete Response (pCR) | absence of active cancer cells in a tissue from the tumor site after NACT |
Non-Pathological Complete Response (non-pCR) | presence of active cancer cells in a tissue from the tumor site after the treatment |

  • The purpose of the study: to investigate whether circulating exosomal microRNAs could predict pCR in breast cancer patients treated with NACT
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Introduction: pCR & nonpCR

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Materials and methods: Flowchart

Methods: Metadata & Describe

Methods: Describe

Methods: Gene Expression Analysis

Methods: Virtual pull-down and Gene Enrichement Analysis

  • Virtual pull-down:
library(DiscoNet)
network_pCR <- virtual_pulldown(
  seed_nodes = seed, 
  database = string_database, 
  id_type = "hgnc", 
  string_confidence_score = 700) # default value
  • Community detection
library(DiscoNet)
communities_list <- community_detection(
  graph_object, 
  algorithm = "mcode", # specifies algorithm, in this case MCODE
  D = 0.05, # threshold of weight percentage of the vertex to be use by MCODE standard value
  haircut = TRUE) # removes the nodes that are only connected to a single node in the community detected
  • Over representation analysis
library(fgsea)

ora_result_nonpCR <- fora(
    pathways = biological_process_list, 
    genes = gense_in_each_community, 
    universe = all_genes_in_analysis, 
    minSize = 10
)

Results: Gene Expression Analysis

Results: Virtual pull-down

  • Pre vs. Post Treatment:
    • The nonpCR Group has 5 potential complexes or networks with upregulated or downregulated activity when comparing pre- and post-treatment
    • The pCR Group has 11 potential complexes or networks with upregulated or downregulated activity when comparing pre- and post-treatment
  • Example plots:

Results: Gene Enrichement Analysis

  • For each relevant community in pCR and non_pCR the main enriched biological processes were identified
  • Representative plots:

Discussion and Conclusion